rs104895441
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001370466.1(NOD2):c.2139C>A(p.Ile713=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. I713I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001370466.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOD2 | NM_001370466.1 | c.2139C>A | p.Ile713= | synonymous_variant | 4/12 | ENST00000647318.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOD2 | ENST00000647318.2 | c.2139C>A | p.Ile713= | synonymous_variant | 4/12 | NM_001370466.1 | P1 | ||
NOD2 | ENST00000300589.6 | c.2220C>A | p.Ile740= | synonymous_variant | 4/12 | 1 | |||
NOD2 | ENST00000641284.2 | c.2139C>A | p.Ile713= | synonymous_variant, NMD_transcript_variant | 4/6 | ||||
NOD2 | ENST00000646677.2 | c.2139C>A | p.Ile713= | synonymous_variant, NMD_transcript_variant | 4/13 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152268Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461716Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727174
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74396
ClinVar
Submissions by phenotype
Regional enteritis;C5201146:Blau syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 12, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at